This may seem like a silly question, but it's an easy option to miss: Have you tried filtering it with just "Wanted" marked on? By default, all three options "Wanted, Collected, and Excluded" are checked on and it might be why all pets are showing up.

The add-on "Pet Tracker" puts all the pets you need to collect right on your map. You can configure it to see all pets in the zone, the pets missing from your collection, or only pets you don't have maximized (rare); or you can turn it off altogether.

This along with an add-on like Petjournal Enhanced, or Pet Theory, and you can find anything in or not in your collection. Petjournal Enhanced has a much more configurable collection search; but you may like Pet Theory if you want something more simplified (and Pet Theory shows a blue box around the primary wild pet you're battling, if it's rare). Just don't use these two addons together at the same time as they conflict. I use Pet Theory, and keep Enhanced off, but ready if I need to do a deeper search for some reason.